CePa (version 0.8.1)

get.cepa: get single cepa object from cepa.all object

Description

get single cepa object from cepa.all object

Usage

get.cepa(x, id = NULL, cen = 1)

Arguments

x

a cepa.all object

id

index or the name of the pathway

cen

index or the name of the centrality

Author

Zuguang Gu <[e-mail]>

Details

The `cepa.all object contains the result for pathways under several centrality measurements. In cepa.all object, each pathway under a specific centrality is a single cepa object. The get.cepa function is used to get the cepa object from the cepa.all object.

See Also

cepa, cepa.all

Examples

if (FALSE) {
data(PID.db)

# ORA extension
data(gene.list)
# will spend about 20 min
res.ora = cepa.all(dif = gene.list$dif, bk = gene.list$bk, pc = PID.db$NCI)
ora = get.cepa(res.ora, id = 5, cen = 3)

# GSA extension
# P53_symbol.gct and P53_cls can be downloaded from
# http://mcube.nju.edu.cn/jwang/lab/soft/cepa/
eset = read.gct("P53_symbol.gct")
label = read.cls("P53.cls", treatment="MUT", control="WT")
# will spend about 45 min
res.gsa = cepa.all(mat = eset, label = label, pc = PID.db$NCI)
gsa = get.cepa(res.gsa, id = 5, cen = 3)
}